Hello @draganb, welcome to the group.
gSender has a calibration tool that you can use to determine how far to move a Y rail to be square. The problem is “How do you move your mill by 1.42mm?”. The best answer that I’ve seen is to mount the LongMill’s Y rails on strips of MDF that have a some slots in them. Then using the slots and some bolt holes you fasten the the strips to the table. I just remounted my LongMill about a week or two ago and did it that way. According to gSender my original mounting was about 1mm off. Now it’s as close as I can measure. I posted about the remount with some pics.
I’ve started to use dial calipers to measure the diameter of my bits and then enter that into the CAD/CAM tool database. You’ll still need to do some trial and error if your trying to make parts fit together. Due to the resistance to cutting, machine flex etc, holes tend to come out small and profiles a bit big and the difference can change with whatever material your using. I was just doing some tests to try dog holes in my spoil board with 3D printed dogs. I decided to use 20mm diameter holes. I needed to cut the holes at 20.25mm and print the dogs at 19.7mm in order to get something that didn’t wiggle to much but was still removable.
If your trying to cut the same square in the same location on your mill I think homing with sensors/switches is the way to go. If it doesn’t need to happen in the same place then using a probe block and mounting the mill and work square should do if you save the files used.